Determination of the physical locations of genes and DNA segments on individual chromosomes is an important aspect of genome research. Correct orientation and ordering of these markers are also crucial in identification of disease genes on the basis of chromosome location. Besides crude mapping methods, such as the use of interspecific somatic cell hybrids containing various subsets or portions of human chromosomes, isotope-labelled probe hybridization to genomic DNA in metaphase chromosomes presents a direct approach to localization of genes to specific chromosomal regions with high precision. In combination with fluorescence-labelling, the resolving power of in situ hybridization has been greatly improved; it is also possible to assign relative positions of genes and DNA segments as close as 1-2 megabase (Mb) apart.
More recently, the introduction of fluorescence in situ hybridization (FISH) with less-condensed chromatin of interphase nuclei or pronuclei further increases the resolution, to around 50-100kb. A major limitation of FISH mapping with interphase nuclei, however, is that the chromatin fibers are organized three-dimensionally, so that gene order can only be inferred by estimating the maximal distance between two probes. Interphase FISH mapping becomes less accurate as the distances between probes increases and the interpretation is complex for multiple fluorescent-conjugate data. On the other hand, although methods such as pulsed field gel electrophoresis and cloning with yeast artificial chromosomes often permit accurate short-range ordering of specific genomic regions, these techniques will have limited applications for the entire genome until sufficient evenly spaced probes are available.